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- PDB-6fsz: Structure of the nuclear RNA exosome -

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Entry
Database: PDB / ID: 6fsz
TitleStructure of the nuclear RNA exosome
Components
  • (Exosome complex component ...) x 9
  • (Exosome complex exonuclease ...) x 2
  • ATP-dependent RNA helicase DOB1
  • Exosome complex protein LRP1
  • M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog
  • RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsRNA / RNA exosome / Ribosome / pre-ribosome / Mtr4 / Helicase
Function / homology
Function and homology information


regulation of exoribonuclease activity / ncRNA polyadenylation / ncRNA 3'-end processing / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / TRAMP complex / 3'-5' RNA helicase activity / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / maturation of 5.8S rRNA / nuclear polyadenylation-dependent antisense transcript catabolic process ...regulation of exoribonuclease activity / ncRNA polyadenylation / ncRNA 3'-end processing / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / TRAMP complex / 3'-5' RNA helicase activity / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / maturation of 5.8S rRNA / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' / nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription / nuclear polyadenylation-dependent CUT catabolic process / U1 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear retention of pre-mRNA at the site of transcription / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / nuclear retention of unspliced pre-mRNA at the site of transcription / CUT catabolic process / nuclear polyadenylation-dependent rRNA catabolic process / nuclear exosome (RNase complex) / exosome (RNase complex) / nuclear polyadenylation-dependent tRNA catabolic process / U4 snRNA 3'-end processing / polyadenylation-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear mRNA surveillance / nuclear-transcribed mRNA catabolic process, non-stop decay / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / histone mRNA catabolic process / rRNA metabolic process / rRNA catabolic process / Hydrolases, Acting on ester bonds, Endoribonucleases producing 5'-phosphomonoesters / nonfunctional rRNA decay / exonucleolytic catabolism of deadenylated mRNA / poly(A) binding / poly(U) RNA binding / RNA catabolic process / Hydrolases, Acting on ester bonds, Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / mRNA catabolic process / enzyme regulator activity / endoribonuclease activity / single-stranded RNA binding / mRNA processing / RNA helicase / double-stranded RNA binding / double-stranded DNA binding / tRNA binding / endonuclease activity / manganese ion binding / mRNA binding / oxidoreductase activity / protein-containing complex binding / nucleolus / nucleotide binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
rRNA-processing arch domain / ATP-dependent RNA helicase Ski2, C-terminal / PNPase/RNase PH domain superfamily / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Exosome complex component, N-terminal domain / rRNA-processing arch domain / RNA-binding domain, S1 / Ribonuclease II/R, conserved site / Ribosomal protein S5 domain 2-type fold / Exosome complex component CSL4, C-terminal ...rRNA-processing arch domain / ATP-dependent RNA helicase Ski2, C-terminal / PNPase/RNase PH domain superfamily / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Exosome complex component, N-terminal domain / rRNA-processing arch domain / RNA-binding domain, S1 / Ribonuclease II/R, conserved site / Ribosomal protein S5 domain 2-type fold / Exosome complex component CSL4, C-terminal / M-phase phosphoprotein 6 / ATP-dependent RNA helicase Ski2-like / Exoribonuclease, phosphorolytic domain 2 / Helicase superfamily 1/2, ATP-binding domain / Exosome-associated factor Rrp6, N-terminal / PIN-like domain superfamily / Nucleic acid-binding, OB-fold / Ribonuclease H-like superfamily / DEAD/DEAH box helicase domain / Prismane-like superfamily / Exosome-associated factor Rrp47/DNA strand repair C1D / HRDC-like superfamily / Sas10/Utp3/C1D / K Homology domain, type 1 / S1 domain / PIN domain / HRDC domain / Ribonuclease II/R / P-loop containing nucleoside triphosphate hydrolase / Exosome complex component RRP45 / Exoribonuclease, phosphorolytic domain 1 / Exosome component EXOSC1/CSL4 / DSHCT (NUC185) domain / Helicase conserved C-terminal domain / DEAD/DEAH box helicase / Sas10/Utp3/C1D family / PMC2NT (NUC016) domain / 3'-5' exonuclease / HRDC domain / Dis3-like cold-shock domain 2 (CSD2) / Rrp44-like cold shock domain / S1 domain / PIN domain / RNB domain / Exosome complex exonuclease RRP4 N-terminal region / Exosome complex component Rrp43 / Exosome complex exonuclease Rrp40 N-terminal domain / KH domain / 3' exoribonuclease family, domain 2 / 3' exoribonuclease family, domain 1 / Dis3-like cold-shock domain 2 / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex component Csl4 / Rrp40, S1 domain / K Homology domain, type 1 superfamily / Exoribonuclease, PH domain 2 superfamily / Rrp44-like cold shock domain / Exosome complex exonuclease RRP44, S1 domain / Helicase, C-terminal / 3'-5' exonuclease domain
ATP-dependent RNA helicase DOB1 / Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex protein LRP1 / Exosome complex component SKI6 / Exosome complex component RRP42 / Exosome complex component MTR3 / M-phase phosphoprotein 6 homolog / Exosome complex component CSL4 / Exosome complex component RRP45 ...ATP-dependent RNA helicase DOB1 / Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex protein LRP1 / Exosome complex component SKI6 / Exosome complex component RRP42 / Exosome complex component MTR3 / M-phase phosphoprotein 6 homolog / Exosome complex component CSL4 / Exosome complex component RRP45 / Exosome complex exonuclease DIS3 / Exosome complex component RRP40 / Exosome complex exonuclease RRP6 / Exosome complex component RRP46
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsSchuller, J.M. / Falk, S. / Conti, E.
Funding support Belgium, 1items
OrganizationGrant numberCountry
ERCEXORICO Belgium
CitationJournal: Science / Year: 2018
Title: Structure of the nuclear exosome captured on a maturing preribosome.
Authors: Jan Michael Schuller / Sebastian Falk / Lisa Fromm / Ed Hurt / Elena Conti /
Abstract: The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex ...The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60) during 7-to-5.8 rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 particle, which harbors the 5.8 rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 rRNA, captures the 3' extension of the 5.8 rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 substrate to process rRNA during ribosome maturation.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Other / Source and taxonomy / Category: atom_sites / entity_src_gen
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Dec 18, 2019Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

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Assembly

Deposited unit
2: RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
AA: Exosome complex component RRP45
BB: Exosome complex component SKI6
CC: Exosome complex component RRP43
DD: Exosome complex component RRP46
EE: Exosome complex component RRP42
FF: Exosome complex component MTR3
GG: Exosome complex component RRP40
HH: Exosome complex component RRP4
II: Exosome complex component CSL4
JJ: Exosome complex exonuclease DIS3
KK: Exosome complex exonuclease RRP6
LL: Exosome complex protein LRP1
MM: ATP-dependent RNA helicase DOB1
NN: M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog


Theoretical massNumber of molelcules
Total (without water)641,38915
Polymers641,38915
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 1 types, 1 molecules 2

#1: RNA chain RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 7158.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast)

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Exosome complex component ... , 9 types, 9 molecules AABBCCDDEEFFGGHHII

#2: Protein/peptide Exosome complex component RRP45 / / Ribosomal RNA-processing protein 45


Mass: 33799.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP45, YDR280W, D9954.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05636
#3: Protein/peptide Exosome complex component SKI6 / / Extracellular mutant protein 20 / Ribosomal RNA-processing protein 41 / Superkiller protein 6


Mass: 27794.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SKI6, ECM20, RRP41, YGR195W, G7587 / Production host: Escherichia coli (E. coli) / References: UniProt: P46948
#4: Protein/peptide Exosome complex component RRP43 / / Ribosomal RNA-processing protein 43


Mass: 43977.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP43, YCR035C, YCR35C, YCR522 / Production host: Escherichia coli (E. coli) / References: UniProt: P25359
#5: Protein/peptide Exosome complex component RRP46 / / Ribosomal RNA-processing protein 46


Mass: 26913.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP46, YGR095C / Production host: Escherichia coli (E. coli) / References: UniProt: P53256
#6: Protein/peptide Exosome complex component RRP42 / / Ribosomal RNA-processing protein 42


Mass: 29294.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP42, YDL111C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12277
#7: Protein/peptide Exosome complex component MTR3 / / mRNA transport regulator 3


Mass: 27559.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Strain: ATCC 204508 / S288c / Gene: MTR3, YGR158C, G6676 / Production host: Escherichia coli (E. coli) / References: UniProt: P48240
#8: Protein/peptide Exosome complex component RRP40 / / Ribosomal RNA-processing protein 40


Mass: 26778.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP40, YOL142W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08285
#9: Protein/peptide Exosome complex component RRP4 / / Ribosomal RNA-processing protein 4


Mass: 39714.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP4, YHR069C / Production host: Escherichia coli (E. coli) / References: UniProt: P38792
#10: Protein/peptide Exosome complex component CSL4 / / CEP1 synthetic lethal protein 4


Mass: 32805.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CSL4, SKI4, YNL232W, N1154 / Production host: Escherichia coli (E. coli) / References: UniProt: P53859

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Exosome complex exonuclease ... , 2 types, 2 molecules JJKK

#11: Protein/peptide Exosome complex exonuclease DIS3 / Chromosome disjunction protein 3 / Ribosomal RNA-processing protein 44


Mass: 113983.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: DIS3, RRP44, YOL021C, O2197 / Production host: Escherichia coli (E. coli)
References: UniProt: Q08162, Hydrolases, Acting on ester bonds, Exoribonucleases producing 5'-phosphomonoesters, Hydrolases, Acting on ester bonds, Endoribonucleases producing 5'-phosphomonoesters
#12: Protein/peptide Exosome complex exonuclease RRP6 / Ribosomal RNA-processing protein 6


Mass: 84159.586 Da / Num. of mol.: 1 / Details: Inactive point mutant D296N / Mutation: D296N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP6, UNC733, YOR001W / Production host: Escherichia coli (E. coli)
References: UniProt: Q12149, Hydrolases, Acting on ester bonds, Exoribonucleases producing 5'-phosphomonoesters

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Protein/peptide , 3 types, 3 molecules LLMMNN

#13: Protein/peptide Exosome complex protein LRP1 / / Like an rRNA processing protein 1 / Yeast C1D domain-containing protein / rRNA processing protein 47


Mass: 21086.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LRP1, RRP47, YC1D, YHR081W / Production host: Escherichia coli (E. coli) / References: UniProt: P38801
#14: Protein/peptide ATP-dependent RNA helicase DOB1 / mRNA transport regulator MTR4


Mass: 122260.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MTR4, DOB1, YJL050W, J1158 / Production host: Escherichia coli (E. coli) / References: UniProt: P47047, RNA helicase
#15: Protein/peptide M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog / Exosome-associated RNA-binding protein MPP6


Mass: 4101.711 Da / Num. of mol.: 1
Details: Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as ...Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MPP6, YNR024W, N3230 / Production host: Escherichia coli (E. coli) / References: UniProt: P53725

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component

Type: COMPLEX

IDNameEntity IDParent-IDSource
1Nuclear RNA exosome1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 150MULTIPLE SOURCES
2Nuclear RNA exosome2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 151RECOMBINANT
3nucleic acid11NATURAL
Molecular weightExperimental value: NO
Source (natural)

Ncbi tax-ID: 4932 / Organism: Saccharomyces cerevisiae (baker's yeast)

IDEntity assembly-ID
22
33
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 38.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22439 / Symmetry type: POINT

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